Coding & Dev Tools

holobiomicslab Skill

Use when after generating a Chemical Feature Tree from q2-qemistree (or any tree artifact) and before using it for alpha-diversity or beta-diversity phylogenetic analyses.

holobiomicslab Skill

Use when you have a comprehensive target list (containing compounds from both positive and negative ionization modes) but need to screen or detect peaks in a single LC-MS run acquired in a specific polarity mode.

holobiomicslab Skill

Use when when you have raw LC-MS/MS data files in mzML, mzXML, or vendor-specific formats and need to load them into a Java-based mass spectrometry analysis framework for downstream spectral analysis, fragmentation tree computation, or metabolite identification.

holobiomicslab Skill

Use when you have molecular structures (SMILES or graph representations) and need to predict or analyze infrared spectral properties using message passing neural networks.

holobiomicslab Skill

Use when when you have raw mass spectrometry data from diverse instrument vendors (Thermo, Sciex, etc.) and need to harmonize and standardize spectrum-level metadata—including scan information, precursor m/z and charge, and ion selection parameters—into a queryable, vendor-agnostic tabular schema.

holobiomicslab Skill

Use when after generating mzPeak files from prototype implementations (Rust, Python, R, or .NET) or after format conversion, and before integrating files into a mass spectrometry data repository or sharing them with collaborators. Use it when specification compliance is a hard requirement (e.

holobiomicslab Skill

Use when when building or extending a mass spectrometry data parser that must support multiple mzML storage formats (plain .mzML, indexed .mzML.gz, standard-compressed .mzML.

holobiomicslab Skill

Use when when extending the MsBackend virtual class to create a custom backend for mass spectrometry data, and you need to store peak m/z and intensity values as variable-length numeric vectors indexed by spectrum.

holobiomicslab Skill

Use when after converting peak-picker output (from MZmine, XCMS, MS-DIAL, or Compound Discoverer) into LipidMatch-compatible format. Use this skill when you need to verify that the converted file will be successfully read by LipidMatch before proceeding to lipid identification;

holobiomicslab Skill

Use when you need to validate that a published software tool (e.g., MassQL) executes correctly in your environment, reproduce published results, or contribute to development.

holobiomicslab Skill

Use when you have a .msp spectral library file with sparse or incomplete metadata (e.

holobiomicslab Skill

Use when after importing raw mass spectrometry data from mzML, mzXML, msp, MGF, or JSON formats using matchms, when you need to ensure that metadata fields (e.

holobiomicslab Skill

Use when you have mass spectrometry imaging data in multiple vendor or open-source formats and need to programmatically route each file to its correct processing handler based on file extension, avoiding hardcoded conditional chains and enabling extensible format support.

holobiomicslab Skill

Use when you have assembled genomic DNA sequences (contigs in FASTA format, not antiSMASH or BOA output) and corresponding LC-MS/MS data (in MGF, mzXML, mzML, or mzData format) from the same organism, and you want to identify novel RiPPs by linking gene cluster predictions to observed mass spectra.

holobiomicslab Skill

Use when you have raw or preprocessed MS/MS spectra in one of the supported formats (MGF, mzML, mzXML, JSON, MSP, mzXML, pickled matchms objects, or USI) and need to extract peak lists (m/z and intensity pairs) along with metadata (precursor m/z, charge, ionization mode) to feed into MS2Query or.

holobiomicslab Skill

Use when when you have preprocessed mass spectra (peak-filtered, metadata-cleaned) in supported formats (mzML, mzXML, msp, MGF, JSON) and need to compare all or many pairs of spectra to identify similar compounds, search spectral libraries, or build a similarity network for spectral clustering or.

holobiomicslab Skill

Use when you have generated a GNPS mass spectral molecular network (in classical or feature-based mode) and want to annotate network nodes with substructural motifs from MS2LDA or chemical class information.

holobiomicslab Skill

Use when you have raw or peak-picked mass spectrometry data in HDF5 format that needs to be loaded into memory for downstream processing (feature alignment, isotope detection, CCS calibration), or when you need to export annotated feature tables with isotopologue metadata back to HDF5 for archival.

holobiomicslab Skill

Use when processing feature lists from LC- or GC-HRMS data (in mzML format or as custom feature tables with m/z and molecular formula columns) and you need to flag potential PFAS candidates.

holobiomicslab Skill

Use when evaluating whether a mass spectrometry data analysis platform (such as mzmine) provides complete module coverage across all advertised separation and ionisation techniques.

holobiomicslab Skill

Use when you have acquired EI or MS2 library files in MSP format (e.g., from NIST via Lib2NIST export, RIKEN, MoNA, SWGDRUG, or GNPS) and need to read them into R to assign SMILES, retention indices, or combine multiple libraries into a single consolidated MSP file for MS-DIAL.

holobiomicslab Skill

Use when when processing downloaded mass spectral libraries (particularly MoNA EI or MS2 libraries) where SMILES information exists but is embedded in unstructured Comment fields rather than a dedicated SMILES field, or when assigning SMILES from external structure databases (SDF files) to library.

holobiomicslab Skill

Use when releasing a new version of a Python package, validating packaging infrastructure changes, or confirming that distribution channels (PyPI, Bioconda) remain functional after upstream updates. Use it as a gate before finalizing a release to catch installation or import breakage early.

holobiomicslab Skill

Use when a paired omics project JSON document contains genome identifiers (e.g. IMG IDs, NCBI accessions) but lacks corresponding organism names.

holobiomicslab Skill

Use when when your project JSON document contains public identifiers (genome IDs, biosample accessions, etc.) that lack human-readable or linked metadata, and you need to populate those fields programmatically before storage or publication to enable full-text search, validation, or cross-linking.

holobiomicslab Skill

Use when you need to feed chemical formulas into a neural network-based formula scorer (such as MIST-CF) that must learn data-dependent representations of formula structure and composition.

holobiomicslab Skill

Use when you have preprocessed LC-MS intensity data (e.

holobiomicslab Skill

Use when you have centroided LC-MS/MS spectral data (in MGF, mzXML, mzML, or mzData format) and want to identify known or predicted natural product structures present in your sample.

holobiomicslab Skill

Use when you have raw peak tables exported from a tandem mass spectrometry preprocessing tool (e.g. Progenesis, MS-DIAL, or Bruker Metaboscape) and need to integrate them with sample metadata for reproducibility filtering, mispicked-ion removal, or group-based feature exclusion.

holobiomicslab Skill

Use when after computing a sparse pairwise distance matrix from nearest neighbor indexes of MS/MS spectra (in mzML, mzXML, or MGF format), and you need to assign each spectrum to a cluster group for downstream analysis such as peptide identification or spectral library construction.

holobiomicslab Skill

Use when when using mpactr filter functions (e.g., filter_mispicked_ions, filter_group, filter_cv) with R6 reference semantics and uncertain whether the copy_object parameter controls deep copying or in-place modification.

holobiomicslab Skill

Use when you have raw MS2 spectra from a sample and need to collapse them into a single sample-level representation for comparison across multiple samples, particularly when samples have poor feature overlap, strong retention time shifts between LC methods, or were acquired on different mass.

holobiomicslab Skill

Use when after batch correction has been applied to metabolomics data using pooled SQC samples, and you need to retrieve the corrected ratios (compound / internal standard) for quality metrics calculation, internal standard recommendation, concentration estimation, or statistical modelling.

holobiomicslab Skill

Use when apply this filter after feature detection and before downstream statistical analysis when your experimental design includes blank samples (e.

holobiomicslab Skill

Use when you have a normalized peak-abundance matrix from FT-ICR MS data (peaks as rows, samples as columns) and need to compare the number and diversity of detected molecular species across experimental conditions—for example, to test whether inoculation or environmental perturbation alters the.

holobiomicslab Skill

Use when you need to verify that an S4 replacement method (e.g., `mz<-`) in a bioinformatics backend class correctly validates input data using vectorized operations on NumericList or similar container objects, rather than inefficient loops or apply functions.